# GigaDB Changelog

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).

## Unreleased

- Feat #1906: Bastion needs a speed upgrade
- Feat #1874: Add dropbox creation script in git repo
- Feat #1957: Create alternative infrastructure with live data copied
- Fix #1990: The tar function reports error in the bastion server
- Feat #1904: Install commonly use software to bastion server
- Fix #1985: Circular dependency between Gitlab pipeline and the Ansible bastion playbook run
- Security #security/4: Use composer.json in main app instead of templated composer.json.dist

## v4.4.17 - 2025-09-09 - 9f3e2c6b1 - live since 2025-09-10

- Feat #2404: Create gitlab runner on AWS EC2 instance

## v4.4.16 - 2025-08-15 - 6e04c0b9e - live since 2025-08-21

- Fix #2428: AdminUserController should target AdminUserController when validating or rejecting a claim
- Feat #2127: Sort datasets by upload status
- Fix #2299: Delete google analytics category from admin dashboard
- Fix #1713: Make curation log recognize user's full name
- Fix: Disable automatic coderabbit review status message
- Fix #2424: Ensure Gitlab pipeline is marked as "Passed" when no jobs has failed
- Fix #561: Save terms and conditions in the database
- Fix #561: An admin can activate the user account
- Fix #561: Enable csrf protection
- Fix #561: Generate a token for account activation by email
- Fix #561: Separate admin user page from non admin user page
- Security: bump the composer group across 2 directories with 6 updates
- Fix #2016: Avoid adding logs if the curator is not updated

## v4.4.15 - 2025-07-23 - a60aa8aa5 - live since 2025-07-24

- Fix #2390: Web site fails to reconnect to DB server if connections are terminated
- Fix #2415: Remove redundant meta tag robots acceptance tests
- Feat #2231: Add BlueSky social icon to header and footer
- Fix: Add GIGADB_PORT to secrets example file
- Feat #481: Add hyperlink to Gensc.org in FAQ page
- Feat #491: Update FAQ entry about service costs
- Feat #489: Add new FAQ entry "What are the benefits of using GigaDB?"
- Feat #482: Update FAQ "What data storage procedures do you follow?"
- Feat #490, #486, #483, #477, #475, #833: Update FAQ page text content
- Feat #2314: Comment out API endpoints from help page that are temporarily not working
- Feat #2329, #2336, #2344: Add new FAQ entries
- Feat #513, #2190: Create meta tags based on environments
- Fix #2406: Upgrade EOL debian buster to debian bullseye

## v4.4.14 - 2025-07-09- d11b331f1 - live since 2025-07-16

- Fix #2384: Set to 'is publishable' if status check during DOI minting returns a 204 status code
- Feat #1641: Check if the DOI has been minted when the upload status is set to 'Published'
- Feat #2236: Display pre print manuscript on dataset page
- Security dependabot#183: Server-Side Request Forgery in axios
- Security dependabot#195: body-parser vulnerable to denial of service when url encoding is enabled

## v4.4.13 - 2025-06-13 - 26083397b - live since 2025-06-16

- Feat #199: Reorder home page sections
- Feat #199: Add dataset feed to homepage
- Feat #208: Homepage news items section rework
- Feat #2189: Make public pages responsive
- Feat #2326: Configure coderabbitai and provide instructions to focus automated code reviews
- Fix #2251: Add a size validation rule when updating a file
- Fix #2011: Specify which fixtures to use for individual test cases
- Feat gigascience/security#4: Make main composer.json a regular, versioned, manually edited file
- Feat gigascience/security#14: decommission top level group variables interpolation

## v4.4.12 - 2025-06-09 - 641317b01 - live since 2025-06-12

- Fix #2351: Fix server error page message
- Feat #1341: Show maintenance error on 500 errors
- Feat #1892: Update onboarding pages layout
- Feat #2235: Use temporary directory for database volume in CI legacy_test job
- Feat #2235: Create Manuscript and DatasetLog Yii2 models and create a wrapper to use Manuscript Yii2 model with yii1 Form
- Feat #2235: Add a checkbox to determine whether if a manuscript should be considered a pre-print link
- Feat security#13: Upgrade Tideways PHP extension version to `5.19.0` and Daemon version to `1.9.36`
- Feat #798: Update Genomic Dataset Checklist text
- Feat #950: Add Jesse Xiao to team page

## v4.4.11 - 2025-05-21 - 4fdb2fb13 - live since 2025-05-26

- Fix #531: Calculate the total volume of files and display it on the homepage
- Fix #2282: Resend email from welcome page
- Fix #2248: List operation in GigaDB API take into account publication_date as a start data and/or end date
- Feat #549: create commands: check if DOI exists in Datacite + update Datacite api metadata

## v4.4.10 - 2025-05-16 - 07a8f63b2 - live since 2025-05-19

- Fix #2294: Add dedicated username variable for authenticating to email service

## v4.4.9 - 2025-04-30 - fd51be0df - live since 2025-05-14

- Fix #2270: Allow transitions to 'Submitted' and 'DataPending' from any upload status.
- Fix #1955: Edit user without being forced to enter a password + add a password regex

## v4.4.8 - 2025-04-08 - 01de0477b - not deployed to live

- Fix #2033: Create a mockup for all upload statuses except published

## v4.4.7 - 2025-03-26 - 4c548f037 - live since 2025-04-03

- Fix #2241: Restore Sketchfab visualisations alongside 3D models files visualisations
- Fix #2180: Add user in curation log when minting the DOI
- Feat #2066: Wrap edit file attribute form in a modal
- Fix #2203: Update the curation log without requiring a page refresh when minting a DOI
- Fix #1290: Update and save project url and name
- Fix #2187: Make FAQ buttons responsive
- Fix #2116: Make authors ordered as shown in the DOI page in the readme file

## v4.4.6 - 2025-03-04 - 996f55f0e - live since 2025-03-14

- Fix #2178: save xml payload even if minting DOI fails
- Feat #2054: Visualize 3D models locally without relying on sketchfab iframe

## v4.4.5 - 2025-02-24 - cfe6bc63c - live since 2025-02-26 

- Fix #1119: Fix filename column width in dataset page
- Feat #2138: Avoid deleting a type when deleting a dataset type

## v4.4.4 - 2025-02-17 - c17c44843 - live since 2025-02-19

- Fix #2099: Add missing permission for CLOCKSS

## v4.4.3 - 2025-02-03 - c62107e5e - live since 2025-02-05

- Feat #474: Update FAQ "What journals are integrated with GigaDB?"
- Feat #476: Update FAQ "How do I write a ReadMe file?"
- Feat #479: Update FAQ "Why is submission to GigaDB not closely integrated with submission to GigaScience?"
- Feat #524: Add FAQ for BUSCO genome completeness analysis
- Fix #2053: Update RDS policy to allow createDBSnapshot during destroy
- Feat #1897: Upgrade OS version to CentOS Stream 9

## v4.4.2 - 2025-01-13 - 7ad7a106b - live since 2025-01-15

- Fix #1975: Remove empty line at the beginning of the xml result
- Feat #456: Improve DataCite metadata by migrating to Datacite version 4.6
- Fix #1727: Sort files and samples by id in descending order when querying

## v4.4.1 - 2024-12-24 - 51c426dfe - live since 2025-01-02

- Feat #2067: Sort files by size in dataset page
- Feat #372: Save dataset as xml in log
- Feat #1940: Reminting notification text change
- Fix #2061: Allow empty keywords in dataset entry
- Fix #1991: Update and save sample ID when updating
- Feat #2008: Remove Dimensions citation link
- Fix #2074: Update contact website URL
- Feat #2089: Update team members
- Feat #2066: Update file attribute values form layout and add expand button for long values
- Feat #2102: Delete outdated apidocs files
- Feat #1667: Add log entry when minting DOI
- Fix #2094: Make Semgrep-based SAST analyzer available in tagged release
- Feat #701: Code refactoring to separate upload status transitions and notifications to prepare for upload status overhaul
- Security #1867: Update the gitlab static application security testing (SAST) job using the Semgrep-based analyzer

## v4.4.0 - 2024-11-13 - ea1a37cc9 - live since 2024-12-12

- Fix #2066: Max length for attribute value set to 1000 in file admin form
- Feat #1968: Add curators manual for operating tools on bastion server and improve tools usage
- Feat #1750: Switch to guzzle instead of cURL (preliminry work to prepare for DataCite schema upgrade)
- Fix #2042: Batch deletion of file attributes and samples to make deleting files from the admin dashboard faster

## v4.3.9 - 2024-10-28 - 961f7821a - 2024-11-06

- Fix #1838: switch datepicker format to yyy-mm-dd
- Feat #1768: Alphabetically sorted dataset author dropdown options in adminDatasetAuthor form
- Fix #1843: Add top margin to table footer in dataset page
- Feat #2034: Maximize input text color contrast
- Feat #1993: Update contact address

## v4.3.8 - 2024-10-10 - 8f6f0d074 - live since 2024-10-22

- Feat #1903: Allow user to upload dataset files to wasabi bucket and also s3 glacier bucket for backup
- Feat #1771: Automatically mount EFS access point to bastion and webapp servers
- Fix #1861: Remove user suffix from wasabi profile and improve curators docs
- Feat #1893: Move new attribute inputs to the end of the adminFile form
- Fix #2048: Upgrade database Dockerfiles from buster to bullseye to fix failed pipeline jobs
- Feat security#2: Upgrade Bootstrap from v3.3.7 to v3.4.1

## v4.3.7 - 2024-09-24 - 7709c8545 - live since 2024-09-26

- Fix #2015: Error when deleting file on admin dasboard
- Fix #2029: Add new file attribute even if edit attribute fields are visible

## v4.3.6 - 2024-09-13 - 2d935c496 -

- Feat #1858: Relabel button that saves attribute in adminFile to avoid ambiguity
- Feat #1849: Able to toggle expand dataset sample attributes field

## v4.3.5 - 2024-08-23 - 4eaa1cda5 - live since 2024-08-29

- Feat #1853: Add tooltips to adminDataset, adminFile and datasetFunder forms
- Fix #1959: Relation cannot be blank error in Dataset:Relation admin form

## v4.3.4 - 2024-08-13 - fd9ed2480 - live since 2024-08-14

- Fix #1908: Correct and improve CI/CD setup documentation
- Fix #1856: Fix overlapping caret and table header in dataset page
- Security #dependabot/114: Command injection in fs-path
- Security #dependabot/115: Remote code execution in handlebars when compiling templates
- Security #dependabot/116: Prototype Pollution in handlebars
- Security #dependabot/172: Unsafe Reflection in base Component class in yiisoft/yii2

## v4.3.3 - 2024-08-05 - 7204ee854 - live since 2024-08-07

- Fix #1848: Save modifications to image metafields
- Feat #1872: Extract stages of postUpload script into separate scripts

## v4.3.2 - 2024-07-22 - 6531115b7 - live since 2024-07-25

- Feat #1892: Remove unused CSS and LESS files
- Fix #1871: Allowed to save species info filling only required inputs

## v4.3.1 - 2024-07-10 - 2ba5e7dbc - live since 2024-07-15

- Feat #1892: Consolidate all layouts into one single layout
- Fix #1912: Enable curators to save Gigadb forms from many browser tabs at once
- Feat #1840: Make create readme tool available as part of postUpload script

## v4.3.0 - 2024-06-25 - 9cf91f224 - live since 2024-07-01

- Feat #1892: Remove old layouts
- Fix #1845: Use file path to update md5 values and file sizes in database
- Fix #1812: Navigating tables on mockup pages does not generate errors
- Fix #1801: Refresh materialized views daily using cron job and drop existing triggers
- Feat #1143: Open external links in new browser tabs
- Feat: updated upload spreadsheet template to version 19
- Fix #1743: Accessibility tweaks on datasetSubmission/upload page

## v4.2.9 - 2024-06-06 - 30a64ce56 - live since 2024-06-11

- Feat #1869: Script to compare files in user dropbox with file list from spreadsheet
- Fix #1825: Remove close button from view new version popup
- Feat #1767: Restyle and reorder the buttons in create / edit dataset admin page

## v4.2.8 - 2024-05-28 - 771372fbb - live since 2024-05-30

- Feat #1832: Make script for calculating the md5 values and file sizes available for bastion users
- Fix #1817: generate mockup link button not appearing for all upload statuses
- Fix #1825: "Continue to view old version" closes New Version Alert pop up
- Feat #514: Add canonical URL to dataset pages

## v4.2.7 - 2024-05-07 - 902e5bfb5 - live since 2024-05-13

- Feat #1834: Create rclone config for bastion users to allow managing files on Wasabi
- Feat #1634, #1824: Add new EC2 server for file serving purposes (including author/reviewer accessible ftp server)
- Fix #1829: Change maintenance window for the daily backup to S3 to prevent DB server error on live web site
- Fix #1831: Update Out-of-date CSP on live blocks javascript scripts to prevent javascript errors

## v4.2.6 - 2024-04-30 - fe0348092 - live since 2024-05-02

- Feat #1394: Update bastion-users Ansible role to create AWS credentials file from Wasabi credentials CSV
- Fix #1833: Files metadata console containers built using gitlab-config-live-build.yml are tagged with "staging"

## v4.2.5 - 2024-04-25 - ca6d17e0f

- Feat #1770: Make AWS EFS can be mounted on the bastion server manually
- Feat #1783: Avoid URLs with double pagination in dataset url
- Feat #1757: Add pagination to samples table in dataset view
- Fix #1800: Read the correct sample page from cache on samples tables
- Feat #1163: Add carets to sortable headers in dataset page
- Feat #1664: Enable post upload script to work with non-published datasets

## v4.2.4 - 2024-04-16 - 576757f38 - live since 2024-04-17

- Docs #1791: Update IAM EC2 policy to prevent permission error when changing EC2 instant type on the fly
- Docs #1786: Add documentation for creating TLS certificate for AWS gigadb.org migration
- Fix #1784: Correct our configuration of PHP-FPM, Nginx and APCu to support real live load
- Feat #1221: EFS filesystem for GigaDB
- Feat #1717 #1715 #1716: remove Google Plus link, update X logo and add Mastodon link to social media links

## v4.2.3 - 2024-04-08 - f084f51dd

- Feat #1618: FUW - Allow customization of email sent to author after "DataPending" status is set
- Security #1626: FUW - Update node version to the latest recommended to avoid openssl hack. Minimize dependency vulnerabilities.
- Fix #1639: Paginate files and samples SQL queries on dataset pages to avoid running out of memory
- Fix #1593: Display the units of file size based on 1000 byte system

## v4.2.2 - 2024-03-25 - 3cf500fe8 - live since 2024-04-03

- Feat #1759: Replace Google Analytics script by Matomo script in all layouts
- Feat #1652: Update API doc for usage of retrieve known datasets by DOI endpoint

## v4.2.1 - 2024-03-18 - ac7d6168b

- Feat #1613: Add descriptive text, improved button labels and tooltips for user profile uploaded datasets tab
- Fix #1666: Update the datacite credentials and make the Mint DOI button working
- Fix #1230: Improve Excel upload tool by adding new dataset types in dev data
- Fix #1722: Show more button on Dataset:Sample admin page works after filtering
- Fix #1714: Visually hide long description in guide workflow, so that it's only visible to screen readers
- Fix #1657: Fix the broken tests from release 4.2.0, fix curation log form and spreadsheet upload consent checkbox
- Feat #1627: FUW - Migrate to Uppy version 2
- Feat #1629: FUW - Upgrade Element UI to latest version

## v4.2.0 - 2024-02-27 - 017ba8f58 - live since 2024-03-13

- Fix #1659: Remove dependency on abandoned inter-container-communication project and fix broken tests
- Feat #1624: FUW - Migrate to Vue 2.7
- Feat #1334: Improve accessibility of public and admin pages, revamp admin pages styles, sync style guide with updated styles

## v4.1.2 - 2024-02-07 - 9a421a2c - live since 2024-02-08

- Fix #1660: Ensure dataset pages that are not published are not publicly visible

## v4.1.1 - 2024-01-30 - 7bb35726 - live since 2024-02-01

- Fix #1527: Make the postUpload script use the image `production-files-metadata-console:production_environment` in the staging and live environments

## v4.1.0 - 2024-01-24 - d0495bee - live since 2024-01-26

- Fix #1654: Fix AdminDatasetForm acceptance tests
- Feat #1569: Display horizontal scroll bar in dataset files table when required
- Fix #1645: Fix failing ResetPasswordCest for FUW
- Feat #588: Re-enable the old, initial work on File Upload Wizard behind a new Gitlab-based feature flag
- Feat #1384: Improve accessibility of login page: input focus state, form errors, aria labels, required

## v4.0.5 - 2024-01-02 - d4deab10 - live since 2024-01-09

- Feat #1595: Update total volume of data on home page
- Fix #1529: Reload the same admin form page after save for private dataset
- Feat #1259: Document how to update dataset spreadsheet template

## v4.0.4 - 2023-12-11 - 4c91cfc

- Feat #1586: Make terraform always look for the latest CentOS Stream 8 x86_64 AMI
- Feat #1530: Implement scenario for checking the updated values in the mockup page

## v4.0.3 - 2023-12-04 - c2869d0

- Fix #1561: show app version in footer on AWS deployment
- Feat #1420: Save bastion user's public key to gitlab variable page
- Feat #1456: Fix footer positioning to viewport bottom
- Feat #1423: Create bash script to update dataset and file links to Wasabi URLs

## v4.0.2 - 2023-11-27 - cba0ca7a

- Fix #1528: Do not use caching on mockup pages

## v4.0.1 - 2023-11-20 - 57129850

- Fix #1562: Make live tideways jobs only available in the tagged GitLab pipeline
- Feat #1365: Improve accessibility of header

## v4.0.0 - 2023-11-06 - 9c012f7b

- Fix #1416: Enable Gitlab tag pipeline and document release process
- Feat #1362: Add "skip to main" link
- Fix #1444: Make tideways build and deploy automatically for the production staging gigadb website
- Docs #1421: Update production deployment SOP, investigate terraform state synchronisation issues and create troubleshooting guide for the deployment process
- Feat #1460: Admin dashboard updated to same more modern look as the public side
- Fix #1102: On sample admin form, save all valid sample attributes while showing errors for non-existent attributes
- Feat #1434: Setup playwright local environment for automated accessibility testing
- Feat #1443: Make ansible playbooks can execute plays separately by adding tags
- Fix #1428: Increase resilience of provisioning by extracting saving EC2 IP addresses as standalone bootstrap plays
- Feat #1368: Improve accessibility of About Page
- Fix #1483: Fix URL creation for ftp_site field in dataset table when using files metadata console tool
- Feat #1374: Improve accessibility and use of semantic html of search results card
- Fix #1449: Fix issue preventing deployment to live production environment bastion server
- Fix #1102: Display error message when creating a sample object or updating an existing sample object with attribute not found in attribute table, and do not create/save it. Refactored container scanning jobs in gitlab pipeline.
- Feat #1376: Fix heading hierarchy in Contact Page, wrap address in `<address>` element
- Feat #1361: Add general accessible landmarks to layouts
- Feat #1363: Fix color contrast issues in pages with new layouts
- Feat #1309: Implement batch processing functionality for readme tool
- Feat #1356: Delete local bootstrap files and replace them with Bootstrap 2.0.4 from CDN
- Feat #1334: add guest mode for freelancers to spin up local gigadb website without GitLab account
- Fix #1310 and #1311: Copy readme files created by readme tool into the
  gigadb-datasets wasabi bucket.
- Feat #1294: Added tool into files metadata console to update dataset FTP site
  and file location URLs.
- Fix #1277: Fix terraform errors and warnings and update SOPS for database backup restoration
- Fix #1088: Excel spreadsheet upload will not insert non exist sample attribute in the spreadsheet into the database.
- Fix #1338: Enable persistent IP address using EIP for bastion hosts on AWS deployments
- Feat #580: Provision monitoring infrastructure with Prometheus and Grafana
- Feat #1282: Upgraded yii1.1 version to `1.1.28`, yii2 version to `2.0.48.1`, postgreSQL engine version to `14.8`, postgreSQL client version to `14`

## v3.1.0 - 2017-01-18 - 83f9cf8

- for historical record

## v3.0.0 - 2016-05-12 - 5d89e0f

- for historical record